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This page was generated on 2024-02-22 12:48:11 -0500 (Thu, 22 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4657
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4397
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1062/2244HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
karyoploteR 1.29.1  (landing page)
Bernat Gel
Snapshot Date: 2024-02-21 14:10:10 -0500 (Wed, 21 Feb 2024)
git_url: https://git.bioconductor.org/packages/karyoploteR
git_branch: devel
git_last_commit: 2a860f3
git_last_commit_date: 2024-01-11 06:04:35 -0500 (Thu, 11 Jan 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for karyoploteR on nebbiolo1


To the developers/maintainers of the karyoploteR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/karyoploteR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: karyoploteR
Version: 1.29.1
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings karyoploteR_1.29.1.tar.gz
StartedAt: 2024-02-22 00:02:54 -0500 (Thu, 22 Feb 2024)
EndedAt: 2024-02-22 00:11:50 -0500 (Thu, 22 Feb 2024)
EllapsedTime: 535.9 seconds
RetCode: 0
Status:   OK  
CheckDir: karyoploteR.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings karyoploteR_1.29.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/karyoploteR.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘karyoploteR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘karyoploteR’ version ‘1.29.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘karyoploteR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘regioneR’ ‘GenomicRanges’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    NEW FEATURES
  Cannot process chunk/lines:
    SIGNIFICANT USER-VISIBLE CHANGES
  Cannot process chunk/lines:
    NEW FEATURES
  Cannot process chunk/lines:
    SIGNIFICANT USER-VISIBLE CHANGES
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
kpPlotDensity     31.152  6.069  37.287
kpPlotGenes       20.031  0.831  20.863
mergeTranscripts  15.254  0.072  15.327
kpPlotHorizon     13.663  0.194  13.856
kpPlotRegions     11.482  0.275  11.758
kpPlotBAMCoverage  7.581  0.192   7.773
kpPlotTranscripts  5.814  0.064   5.877
kpPlotManhattan    5.165  0.076   5.242
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/karyoploteR.Rcheck/00check.log’
for details.



Installation output

karyoploteR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL karyoploteR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘karyoploteR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (karyoploteR)

Tests output

karyoploteR.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(karyoploteR)
Loading required package: regioneR
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
> 
> test_check("karyoploteR")
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 177 ]

══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• empty test (3): 'test_plotKaryotype.R:27:1', 'test_plotKaryotype.R:34:1',
  'test_plotKaryotype.R:44:1'

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 177 ]
> 
> proc.time()
   user  system elapsed 
 18.913   1.876  20.781 

Example timings

karyoploteR.Rcheck/karyoploteR-Ex.timings

nameusersystemelapsed
addGeneNames3.0950.0963.192
autotrack0.0010.0000.001
colByCategory0.0030.0000.002
colByChr0.4640.0000.464
colByRegion0.9860.1191.106
colByValue0.1860.0010.186
darker0.0010.0000.001
filterParams0.0010.0000.001
findIntersections0.1190.0000.119
getChromosomeNamesBoundingBox0.0490.0000.049
getColorSchemas0.0000.0030.003
getCytobandColors0.0020.0000.002
getCytobands0.0020.0010.002
getDataPanelBoundingBox0.0440.0000.044
getDefaultPlotParams0.0670.0070.075
getMainTitleBoundingBox0.0360.0000.036
getTextSize0.0720.0030.076
getVariantsColors0.0010.0000.001
horizonColors0.0030.0010.003
is.color0.0010.0000.001
kpAbline1.0510.0351.088
kpAddBaseNumbers0.3130.0010.314
kpAddChromosomeNames0.0340.0000.035
kpAddChromosomeSeparators0.4080.0000.408
kpAddColorRect0.1390.0000.139
kpAddCytobandLabels0.3920.0000.392
kpAddCytobands0.0310.0000.031
kpAddCytobandsAsLine0.0670.0000.067
kpAddLabels0.370.020.39
kpAddMainTitle0.0310.0000.031
kpArea0.3090.0040.313
kpArrows0.5300.0040.534
kpAxis0.2790.0000.279
kpBars0.1770.0040.181
kpDataBackground0.2180.0040.222
kpHeatmap0.1350.0000.135
kpLines0.2740.0000.274
kpPlotBAMCoverage7.5810.1927.773
kpPlotBAMDensity1.8500.0241.874
kpPlotBigWig1.8750.0841.960
kpPlotCoverage0.3650.0000.365
kpPlotDensity31.152 6.06937.287
kpPlotGenes20.031 0.83120.863
kpPlotHorizon13.663 0.19413.856
kpPlotLinks0.8980.0000.897
kpPlotLoess0.1030.0000.103
kpPlotManhattan5.1650.0765.242
kpPlotMarkers1.5240.0241.548
kpPlotNames0.1080.0000.108
kpPlotRainfall0.7370.0280.766
kpPlotRegions11.482 0.27511.758
kpPlotRibbon0.0750.0040.079
kpPlotTranscripts5.8140.0645.877
kpPoints0.2360.0050.240
kpPolygon0.1900.0000.191
kpRect0.6490.0080.657
kpSegments0.5080.0240.531
kpText0.2340.0040.237
lighter0.0010.0000.001
makeGenesDataFromTxDb2.8530.0752.929
mergeTranscripts15.254 0.07215.327
plotDefaultPlotParams0.1470.0000.147
plotKaryotype0.9870.0481.036
plotPalettes0.0160.0030.019
prepareParameters20.0340.0000.034
prepareParameters40.0330.0040.038
processClipping0.0360.0000.036
transparent0.0010.0000.001